To evaluate the efficacy of local drug delivery of 2% Minocycline Hydrochloride (HCL) ointment as an adjunctive in non-surgical periodontal treatment. This pilot study, a clinical trial, included 9 periodontitis patients who completed the hygienic phase of periodontal treatment and enrolled in supportive periodontal therapy. All of the participants had two or more sites of remaining periodontal probing depth (PPD) > 5 mm in bilateral quadrants. Twenty-two sites were selected and randomly allocated for 2% Minocycline HCL ointment application (test group) and non-application (control group) with a split-mouth design. 2% Minocycline HCL ointment was applied in 11 sites of PPD at days 0, 14, and 28. The clinical parameters; PPD, gingival margin (GM), and clinical attachment level (CAL) were recorded at the baseline and evaluation (4 weeks after last application) in both groups. There was no statistically significant difference in PPD and CAL at the baseline between the control and the test group. The test group showed a significantly greater reduction in PPD and CAL gain between the baseline and evaluation. The PPD reduction in the control groups between the baseline and evaluation revealed a statistically significant difference. However, no statistically significant difference in CAL gain was observed between the baseline and evaluation in the control group. The data suggested that subgingival administration of Minocycline ointment after non-surgical periodontal treatment might be helpful in PPD reduction and CAL gain within the first month after administration.